Related papers: Explicit formulas for reaction probability in reac…
A combination of reaction-diffusion models with moving-boundary problems yields a system in which the diffusion (spreading and penetration) and reaction (transformation) evolve the system's state and geometry over time. These systems can be…
Finding optimal reaction coordinates and predicting accurate kinetic rates for activated processes are two of the foremost challenges of molecular simulations. We introduce an algorithm that tackles the two problems at once: starting from a…
Stochastic reaction-diffusion models are employed to represent many complex physical, biological, societal, and ecological systems. The macroscopic reaction rates describing the large-scale kinetics in such systems are effective,…
We created an efficient algorithm suitable for graphics processing units (GPUs) to perform Monte Carlo simulations of a subset of reaction-diffusion models. The algorithm uses techniques that are specific to GPU programming, and combines…
Several algorithms have been used for mass transfer between particles undergoing advective and macro-dispersive random walks. The mass transfer between particles is required for general reactions on, and among, particles. The mass transfer…
The phase transitions classes of reaction-diffusion systems with multi-particle reactions is an open challenging problem. Large scale simulations are applied for the 3A -> 4A, 3A -> 2A and the 3A -> 4A, 3A->0 triplet reaction models with…
Density Functional Theory (DFT) calculations are being routinely used to identify new material candidates that approach activity near fundamental limits imposed by thermodynamics or scaling relations. DFT calculations have finite…
By considering the master equation of the partially asymmetric diffusion process on a one-dimensional lattice, the most general boundary condition (i.e. interactions) for the multi-species reaction-diffusion processes is considered.…
A mesoscopic multi-particle collision model for fluid dynamics is generalized to incorporate the chemical reactions among species that may diffuse at different rates. This generalization provides a means to simulate reaction-diffusion…
We analyze the efficiency of different methods for the calculation of reaction rates in the case of two simple analytical benchmark systems. Two classes of methods are considered: the first are based on the free energy calculation along a…
A one-dimensional reaction-diffusion model consisting of two species of particles and vacancies on a ring is introduced. The number of particles in one species is conserved while in the other species it can fluctuate because of creation and…
One-dimensional reaction-diffusion systems are mapped through a similarity transformation onto integrable (and a priori non-stochastic) quantum chains. Time-dependent properties of these chemical models can then be found exactly. The…
We formulate empirically the rapidity density distribution of produced particles in multiple particle production. The assumed mechanism is that the produced particles are emitted isotropically from several emitting centers, located on the…
An idea for evaluating transition probabilities in chemical reaction systems is proposed, which is efficient for repeated calculations with various rate constants. The idea is based on duality relations; instead of direct time-evolutions of…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
Magnetic reconnection is thought to be the driver for many explosive phenomena in the universe. The energy release and particle acceleration during reconnection have been proposed as a mechanism for producing high-energy emissions and…
We propose the deterministic rate equation of three-species in the reaction - diffusion system. For this case, our purpose is to carry out the decay process in our three-species reaction-diffusion model of the form $A+B+C\to D$. The…
The distribution of the electric microfield at a charged particle moving in a two-component plasma is calculated. The theoretical approximations are obtained via the parameter integration technique and using the screened pair approximation…
Most of the published articles on random motions have been devoted to the study of the telegraph process or its generalizations that describe the random motion in $R^n$ of a single particle in a Markov or semi-Markov medium. However, up to…
An inversion method is formulated for extracting entanglement-related information on two-particle interactions in a one-dimensional system from measurable one-particle position- and momentum-distribution functions. The method is based on a…